Journal Issue: Algorithms Mol Biol Volume 19;  2024

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Journal List

Volume 19;  2024

Research

Investigating the complexity of the double distance problems
Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
Algorithms Mol Biol. 2024; 19: 1. Published online 2024 Jan 4. doi: 10.1186/s13015-023-00246-y
PMCID:
PMC10765962
Abstract Article PDF–2.7M
Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem
Junyan Dai, Tobias Rubel, Yunheng Han, Erin K. Molloy
Algorithms Mol Biol. 2024; 19: 2. Published online 2024 Jan 8. doi: 10.1186/s13015-023-00249-9
PMCID:
PMC10775561
Abstract Article PDF–2.0M
Fulgor: a fast and compact k-mer index for large-scale matching and color queries
Jason Fan, Jamshed Khan, Noor Pratap Singh, Giulio Ermanno Pibiri, Rob Patro
Algorithms Mol Biol. 2024; 19: 3. Published online 2024 Jan 22. doi: 10.1186/s13015-024-00251-9
PMCID:
PMC10810250
Abstract Article PDF–2.3M
Co-linear chaining on pangenome graphs
Jyotshna Rajput, Ghanshyam Chandra, Chirag Jain
Algorithms Mol Biol. 2024; 19: 4. Published online 2024 Jan 27. doi: 10.1186/s13015-024-00250-w
PMCID:
PMC11288099
Abstract Article PDF–2.6M
Global exact optimisations for chloroplast structural haplotype scaffolding
Victor Epain, Rumen Andonov
Algorithms Mol Biol. 2024; 19: 5. Published online 2024 Feb 6. doi: 10.1186/s13015-023-00243-1
PMCID:
PMC11288059
Abstract Article PDF–5.4M
Predicting horizontal gene transfers with perfect transfer networks
Alitzel López Sánchez, Manuel Lafond
Algorithms Mol Biol. 2024; 19: 6. Published online 2024 Feb 6. doi: 10.1186/s13015-023-00242-2
PMCID:
PMC10848447
Abstract Article PDF–2.2M
Unifying duplication episode clustering and gene-species mapping inference
Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka, Jarosław Paszek
Algorithms Mol Biol. 2024; 19: 7. Published online 2024 Feb 14. doi: 10.1186/s13015-024-00252-8
PMCID:
PMC10865717
Abstract Article PDF–2.8M
Recombinations, chains and caps: resolving problems with the DCJ-indel model
Leonard Bohnenkämper
Algorithms Mol Biol. 2024; 19: 8. Published online 2024 Feb 27. doi: 10.1186/s13015-024-00253-7
PMCID:
PMC10900646
Abstract Article PDF–2.6M
SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration
Mateo Gray, Sebastian Will, Hosna Jabbari
Algorithms Mol Biol. 2024; 19: 9. Published online 2024 Mar 3. doi: 10.1186/s13015-024-00256-4
PMCID:
PMC11289965
Abstract Article PDF–2.6M
Finding maximal exact matches in graphs
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Algorithms Mol Biol. 2024; 19: 10. Published online 2024 Mar 11. doi: 10.1186/s13015-024-00255-5
PMCID:
PMC10929130
Abstract Article PDF–2.7M
Suffix sorting via matching statistics
Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi
Algorithms Mol Biol. 2024; 19: 11. Published online 2024 Mar 12. doi: 10.1186/s13015-023-00245-z
PMCID:
PMC10935992
Abstract Article PDF–2.5M
Median quartet tree search algorithms using optimal subtree prune and regraft
Shayesteh Arasti, Siavash Mirarab
Algorithms Mol Biol. 2024; 19: 12. Published online 2024 Mar 13. doi: 10.1186/s13015-024-00257-3
PMCID:
PMC10938725
Abstract Article PDF–3.1M
Infrared: a declarative tree decomposition-powered framework for bioinformatics
Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty, Sebastian Will
Algorithms Mol Biol. 2024; 19: 13. Published online 2024 Mar 16. doi: 10.1186/s13015-024-00258-2
PMCID:
PMC10943887
Abstract Article PDF–3.6M
Space-efficient computation of k-mer dictionaries for large values of k
Diego Díaz-Domínguez, Miika Leinonen, Leena Salmela
Algorithms Mol Biol. 2024; 19: 14. Published online 2024 Apr 5. doi: 10.1186/s13015-024-00259-1
PMCID:
PMC10996146
Abstract Article PDF–3.6M
Pfp-fm: an accelerated FM-index
Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie
Algorithms Mol Biol. 2024; 19: 15. Published online 2024 Apr 10. doi: 10.1186/s13015-024-00260-8
PMCID:
PMC11005213
Abstract Article PDF–2.7M
Fast, parallel, and cache-friendly suffix array construction
Jamshed Khan, Tobias Rubel, Erin Molloy, Laxman Dhulipala, Rob Patro
Algorithms Mol Biol. 2024; 19: 16. Published online 2024 Apr 28. doi: 10.1186/s13015-024-00263-5
PMCID:
PMC11056320
Abstract Article PDF–2.4M
Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants
Yutong Qiu, Yihang Shen, Carl Kingsford
Algorithms Mol Biol. 2024; 19: 17. Published online 2024 Apr 29. doi: 10.1186/s13015-024-00262-6
PMCID:
PMC11056321
Abstract Article PDF–3.9M
NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model
Yushu Liu, Mohammadamin Edrisi, Zhi Yan, Huw A Ogilvie, Luay Nakhleh
Algorithms Mol Biol. 2024; 19: 18. Published online 2024 Apr 29. doi: 10.1186/s13015-024-00264-4
PMCID:
PMC11059640
Abstract Article PDF–3.7M
ESKEMAP: exact sketch-based read mapping
Tizian Schulz, Paul Medvedev
Algorithms Mol Biol. 2024; 19: 19. Published online 2024 May 4. doi: 10.1186/s13015-024-00261-7
PMCID:
PMC11069465
Abstract Article PDF–2.0M
Compression algorithm for colored de Bruijn graphs
Amatur Rahman, Yoann Dufresne, Paul Medvedev
Algorithms Mol Biol. 2024; 19: 20. Published online 2024 May 26. doi: 10.1186/s13015-024-00254-6
PMCID:
PMC11129398
Abstract Article PDF–1.6M
Metric multidimensional scaling for large single-cell datasets using neural networks
Stefan Canzar, Van Hoan Do, Slobodan Jelić, Sören Laue, Domagoj Matijević, Tomislav Prusina
Algorithms Mol Biol. 2024; 19: 21. Published online 2024 Jun 11. doi: 10.1186/s13015-024-00265-3
PMCID:
PMC11165904
Abstract Article PDF–2.9M
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